Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics

Abstract

A substantial portion of the primate genome is composed of non-coding regions, so-called “dark matter”, which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

“…Repetitive sequences are present at a higher abundance in distinct loci of specialized chromosomes, such as microchromosomes, supernumerary chromosomes, and sex chromosomes compared with autosomes [ 25 , 34 , 51 ]. Snakes present high diversity, especially in their sex-determining strategies, making them an interesting group for investigating the evolutionary trajectories of sex chromosomes.…”

“…A common feature of sex chromosomes is the accumulation of repetitive DNA, which accounts for their diversification and evolution. The heterochromatin part is highly enriched in repetitive DNA (TEs and satellites), which can differ substantially in number between sexes [ 30 , 51 , 67 , 68 ]. TEs can play an important role in sex chromosome differentiation [ 69 , 70 , 71 ].…”

“…During their evolution, variations in repeat sequences proliferate and mediate chromosomal rearrangements, resulting in either deleterious or positive effects. Consequently, repeats are interesting markers that can be used to study phylogenetic and taxonomic relationships [ 24 , 50 , 51 , 52 ]. The high level of specificity of repetitive sequences is an important tool for understanding evolutionary dynamics.…”

Repetitive Elements in Humans

“…Furthermore, mitochondrial diseases can be inherited via NUMTs not only via the maternal but also the paternal line: this has been shown in seven families [ 51 ]. The possible influence of satellite DNA copy numbers on human fertility have been previously reported [ 44 , 45 ], while the influence of RNA derived from HORs is still not really understood [ 46 , 52 ]. …”

“…The possible influence of satellite DNA copy numbers on human fertility have been previously reported [ 44 , 45 ], while the influence of RNA derived from HORs is still not really understood [ 46 , 52 ].…”